Contacts of the helix formed by residues 489 - 495 (chain u) in PDB entry 6FF7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 489 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4049 ILE 3.1 9.2 - - - +
4069 TYR* 3.2 17.0 - - + -
4169 TYR* 2.1 33.0 - - + +
4179 ARG* 1.3 35.9 - - - +
4189 GLY* 1.5 54.6 + - - +
4199 PRO 3.9 0.4 - - - -
4219 ALA* 2.1 34.2 - - - +
488u SER* 1.3 59.1 - - - -
490u GLU* 1.3 49.1 - - - +
491u GLU* 4.5 0.7 - - + -
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Residues in contact with GLU 490 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4169 TYR* 3.2 0.8 - - - +
4189 GLY 1.2 56.9 + - - -
4199 PRO* 1.8 32.8 - - + +
4209 LYS 1.4 25.5 + - - -
4219 ALA 1.5 24.5 + - - -
4229 PHE* 1.5 113.5 - - + +
4239 GLN 2.6 0.2 - - - +
489u PRO* 1.3 43.5 - - - +
491u GLU 1.3 43.5 - - - -
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Residues in contact with GLU 491 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4009 HIS 3.4 3.5 - - - +
4019 GLY* 2.4 34.1 - - - +
4049 ILE* 4.7 8.3 - - + -
4179 ARG 4.5 0.4 - - - +
4189 GLY* 0.9 47.0 - - - -
4199 PRO* 0.9 133.9 - - + +
4209 LYS 2.2 12.9 + - - -
489u PRO* 4.5 2.5 - - + -
490u GLU 1.3 28.5 - - - -
492u GLN* 1.3 53.7 + - - -
494u GLU* 2.9 14.7 + - - +
495u ARG* 3.0 8.8 + - - +
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Residues in contact with GLN 492 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4009 HIS* 3.9 10.1 - - + +
4019 GLY 3.5 0.2 + - - -
4029 LEU* 3.1 31.9 - - + -
4189 GLY* 3.1 8.2 - - - -
4209 LYS* 1.8 10.0 - - - +
4219 ALA* 4.5 7.6 - - + +
488u SER* 6.1 1.8 - - - -
490u GLU 3.0 0.8 + - - -
491u GLU* 1.3 72.0 - - - +
493u LYS* 1.3 51.2 - - - +
495u ARG 3.0 0.7 + - - -
496u LYS* 2.9 30.8 + - - +
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Residues in contact with LYS 493 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4209 LYS* 0.8 183.0 - - - +
4219 ALA* 2.9 2.8 - - - +
4239 GLN* 4.4 5.8 - - + -
4249 ARG* 4.4 7.2 - - + +
492u GLN* 1.3 43.2 - - - +
494u GLU* 1.3 56.0 + - - -
495u ARG 3.2 0.7 + - - -
496u LYS* 3.9 12.7 + - - +
497u ILE 5.2 0.5 + - - -
526u PHE* 5.2 6.3 - - - +
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Residues in contact with GLU 494 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4199 PRO* 3.8 15.3 - - + +
4209 LYS* 2.0 29.5 - - - +
4239 GLN* 5.5 4.3 - - + -
491u GLU 3.3 7.6 - - - +
493u LYS 1.3 66.4 - - - -
495u ARG* 1.3 57.0 + - - +
496u LYS 3.8 0.2 - - - -
497u ILE* 4.9 8.3 - - - +
526u PHE* 4.0 30.2 - - - +
530u PRO* 3.4 30.9 - - + +
531u LEU 5.0 0.7 + - - -
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Residues in contact with ARG 495 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3999 LEU 3.4 7.9 - - - +
4009 HIS* 1.0 88.9 + - - +
4019 GLY* 2.8 6.1 - - - +
491u GLU 3.0 0.8 + - - -
492u GLN 3.0 5.3 + - - -
494u GLU* 1.3 80.8 - - - +
496u LYS* 1.3 62.0 + - - +
497u ILE* 3.1 5.1 + - - +
498u MET* 3.6 10.3 + - - +
499u LYS 4.8 0.3 + - - -
530u PRO* 5.5 3.1 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il